Brain sought to build an alliance between Gecko and Vault City based on power from Gecko being sent to Vault City in exchange for medical research on how to "restore" the ghouls to humanity. Brain was recruiting followers from ghouls and glowing ones living in Gecko, but could not talk to somebody in Vault City because of xenophobia.

The Chosen One can become a Renewal member and work towards completion of Brain's ideas. This includes fixing the reactor, optimising it, and convincing McClure to accept an alliance between the two locations. Unfortunately, a bug prevents play of an ending slide that reflects these choices.